Reading the Underlying Information From Massive Metagenomic Sequencing Data

Zhang, Xuegong; Liu, Shansong; Cui, Henggang; Chen, Ting

doi:10.1109/jproc.2016.2604406

Cited by 14 publications

(14 citation statements)

References 105 publications

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“…The other 57% of cells are microbial (bacteria, viruses, archaea, microeukaryotes), and therefore, in terms of cell abundance at least, humans are actually more microbial than human. This statement is also true when considering ratios of gene abundance-microbial genes within the human body are thought to outnumber human genes by between 150 and 1000 times [15,16]. With a moment of reflection, this can lead to a medley of existential questions such as-what does it mean to be human?…”

Section: Forty-three Percent Humanmentioning

confidence: 99%

Walking Ecosystems in Microbiome-Inspired Green Infrastructure: An Ecological Perspective on Enhancing Personal and Planetary Health

2018

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Principles of ecology apply at myriad scales, including within the human body and the intertwined macro and microscopic ecosystems that we depend upon for survival. The conceptual principles of dysbiosis (‘life in distress’) also apply to different realms of life—our microbiome, the macro environment and the socioeconomic domain. Viewing the human body as a holobiont—a host plus billions of microbial organisms working symbiotically to form a functioning ecological unit—has the potential to enhance personal and planetary health. We discuss this ecological perspective in our paper. We also discuss the proposals to rewild the microbiome, innovative microbiome-inspired green infrastructure (MIGI) and the basis of prescribing ‘doses of nature’. Particular emphasis is given to MIGI—a collective term for the design and management of innovative living urban features that could potentially enhance public health via health-inducing microbial interactions. This concept builds upon the microbiome rewilding hypothesis. Mounting evidence points to the importance of microbial diversity in maintaining favorable health. Moreover, connecting with nature—both physically and psychologically–has been shown to enhance our health and wellbeing. However, we still need to understand the underlying mechanisms, and optimal types and levels of exposure. This paper adds to other recent calls for the inclusion of the environment-microbiome-health axis in nature–human health research. Recognizing that all forms of life—both the seen and the unseen—are in some way connected (ecologically, socially, evolutionarily), paves the way to valuing reciprocity in the nature–human relationship. It is with a holistic and symbiotic perspective that we can begin to integrate strategies and address connected issues of human and environmental health. The prospective strategies discussed in our paper focus on enhancing our connections with the natural world, and ultimately aim to help address the global challenge of halting and reversing dysbiosis in all its manifestations.

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Section: Forty-three Percent Humanmentioning

confidence: 99%

Walking Ecosystems in Microbiome-Inspired Green Infrastructure: An Ecological Perspective on Enhancing Personal and Planetary Health

2018

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“…This review focused on the scientific questions of existing studies, but did not cover much of the bioinformatics methods and tools that are crucial to enable those studies [125]. With the rapid development of next generation sequence techniques, the accumulation of data far exceeds our ability in handling, analyzing and understanding the data.…”

Section: Discussionmentioning

confidence: 99%

An overview of major metagenomic studies on human microbiomes in health and disease

Cui

Zhang

2016

Quant. Biol.

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Many microbes are important symbiotes of human. They form specific microbiota communities, participate in various kinds of biological processes of their host and thus deeply affect human health status. Metagenomic sequencing has been widely used in human microbiota study due to its capacity of studying all genetic materials in an environment as a whole without any extra need of isolation or cultivation of microorganisms. Many efforts have been made by researchers in this area trying to dig out interesting knowledge from various metagenome data. In this review, we go through some prominent studies in the metagenomic area. We summarize them into three categories, constructing taxonomy and gene reference, characterization of microbiome distribution patterns, and detection of microbiome alternations associated with specific human phenotypes or diseases. Some available data resources are also provided. This review can serve as an entrance to this exciting and rapidly developing field for researchers interested in human microbiomes.

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Section: Introductionmentioning

confidence: 99%

“…It is now widely known that microbiomes or the ecological community of microbes living at a certain site of the human host such as the gut can play important roles in human health [1–5]. Metagenomic sequencing is a powerful technology for studying the microbiome by sequencing DNAs from all the genomes of its component microbes [5]. Since it is impossible to capture the full components of a microbiome, a ‘metagenomic sample’ is actually a subset of the target metagenome captured with the sequencing process, as a sample from a population in statistics [6].…”

Section: Introductionmentioning

confidence: 99%

Estimating the total genome length of a metagenomic sample using k-mers

Hua

Zhang

2019

BMC Genomics

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Background Metagenomic sequencing is a powerful technology for studying the mixture of microbes or the microbiomes on human and in the environment. One basic task of analyzing metagenomic data is to identify the component genomes in the community. This task is challenging due to the complexity of microbiome composition, limited availability of known reference genomes, and usually insufficient sequencing coverage. Results As an initial step toward understanding the complete composition of a metagenomic sample, we studied the problem of estimating the total length of all distinct component genomes in a metagenomic sample. We showed that this problem can be solved by estimating the total number of distinct k-mers in all the metagenomic sequencing data. We proposed a method for this estimation based on the sequencing coverage distribution of observed k-mers, and introduced a k-mer redundancy index ( KRI ) to fill in the gap between the count of distinct k-mers and the total genome length. We showed the effectiveness of the proposed method on a set of carefully designed simulation data corresponding to multiple situations of true metagenomic data. Results on real data indicate that the uncaptured genomic information can vary dramatically across metagenomic samples, with the potential to mislead downstream analyses. Conclusions We proposed the question of how long the total genome length of all different species in a microbial community is and introduced a method to answer it. Electronic supplementary material The online version of this article (10.1186/s12864-019-5467-x) contains supplementary material, which is available to authorized users.

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Reading the Underlying Information From Massive Metagenomic Sequencing Data

Cited by 14 publications

References 105 publications

Walking Ecosystems in Microbiome-Inspired Green Infrastructure: An Ecological Perspective on Enhancing Personal and Planetary Health

Walking Ecosystems in Microbiome-Inspired Green Infrastructure: An Ecological Perspective on Enhancing Personal and Planetary Health

An overview of major metagenomic studies on human microbiomes in health and disease

Estimating the total genome length of a metagenomic sample using k-mers

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